@misc{KahlKappelJoshietal.2021,
  author    = {Kahl, Sandra and Kappel, Christian and Joshi, Jasmin Radha and Lenhard, Michael},
  title     = {Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-53003},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-530035},
  pages     = {13986 -- 14002},
  year      = {2021},
  abstract  = {To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.},
  language  = {en}
}
@misc{EldridgeŁangowskiStaceyetal.2016,
  author    = {Eldridge, Tilly and Łangowski, Łukasz and Stacey, Nicola and Jantzen, Friederike and Moubayidin, Laila and Sicard, Adrien and Southam, Paul and Kennaway, Richard and Lenhard, Michael and Coen, Enrico S. and {\O}stergaard, Lars},
  title     = {Fruit shape diversity in the Brassicaceae is generated by varying patterns of anisotropy},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {986},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43804},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438041},
  pages     = {3394 -- 3406},
  year      = {2016},
  abstract  = {Fruits exhibit a vast array of different 3D shapes, from simple spheres and cylinders to more complex curved forms; however, the mechanism by which growth is oriented and coordinated to generate this diversity of forms is unclear. Here, we compare the growth patterns and orientations for two very different fruit shapes in the Brassicaceae: the heart-shaped Capsella rubella silicle and the near-cylindrical Arabidopsis thaliana silique. We show, through a combination of clonal and morphological analyses, that the different shapes involve different patterns of anisotropic growth during three phases. These experimental data can be accounted for by a tissue level model in which specified growth rates vary in space and time and are oriented by a proximodistal polarity field. The resulting tissue conflicts lead to deformation of the tissue as it grows. The model allows us to identify tissue-specific and temporally specific activities required to obtain the individual shapes. One such activity may be provided by the valve-identity gene FRUITFULL, which we show through comparative mutant analysis to modulate fruit shape during post-fertilisation growth of both species. Simple modulations of the model presented here can also broadly account for the variety of shapes in other Brassicaceae species, thus providing a simplified framework for fruit development and shape diversity.},
  language  = {en}
}
@misc{Lenhard2012,
  author    = {Lenhard, Michael},
  title     = {All's well that ends well},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {906},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43803},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438035},
  pages     = {9 -- 11},
  year      = {2012},
  abstract  = {The transition from cell proliferation to cell expansion is critical for determining leaf size. Andriankaja et al. (2012) demonstrate that in leaves of dicotyledonous plants, a basal proliferation zone is maintained for several days before abruptly disappearing, and that chloroplast differentiation is required to trigger the onset of cell expansion.},
  language  = {en}
}
@misc{SasMuellerKappeletal.2016,
  author    = {Sas, Claudia and M{\"u}ller, Frank and Kappel, Christian and Kent, Tyler V. and Wright, Stephen I. and Hilker, Monika and Lenhard, Michael},
  title     = {Repeated inactivation of the first committed enzyme underlies the loss of benzaldehyde emission after the selfing transition in Capsella},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {904},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43801},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438018},
  pages     = {3313 -- 3319},
  year      = {2016},
  abstract  = {The enormous species richness of flowering plants is at least partly due to floral diversification driven by interactions between plants and their animal pollinators [1, 2]. Specific pollinator attraction relies on visual and olfactory floral cues [3-5]; floral scent can not only attract pollinators but also attract or repel herbivorous insects [6-8]. However, despite its central role for plant-animal interactions, the genetic control of floral scent production and its evolutionary modification remain incompletely understood [9-13]. Benzenoids are an important class of floral scent compounds that are generated from phenylalanine via several enzymatic pathways [14-17]. Here we address the genetic basis of the loss of floral scent associated with the transition from outbreeding to selfing in the genus Capsella. While the outbreeding C. grandiflora emits benzaldehyde as a major constituent of its floral scent, this has been lost in the selfing C. rubella. We identify the Capsella CNL1 gene encoding cinnamate: CoA ligase as responsible for this variation. Population genetic analysis indicates that CNL1 has been inactivated twice independently in C. rubella via different novel mutations to its coding sequence. Together with a recent study in Petunia [18], this identifies cinnamate: CoA ligase as an evolutionary hotspot for mutations causing the loss of benzenoid scent compounds in association with a shift in the reproductive strategy of Capsella from pollination by insects to self-fertilization.},
  language  = {en}
}
@misc{PowellLenhard2012,
  author    = {Powell, Anahid E. and Lenhard, Michael},
  title     = {Control of organ size in plants},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {898},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43802},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-438029},
  pages     = {10},
  year      = {2012},
  abstract  = {The size of plant organs, such as leaves and flowers, is determined by an interaction of genotype and environmental influences. Organ growth occurs through the two successive processes of cell proliferation followed by cell expansion. A number of genes influencing either or both of these processes and thus contributing to the control of final organ size have been identified in the last decade. Although the overall picture of the genetic regulation of organ size remains fragmentary, two transcription factor/microRNA-based genetic pathways are emerging in the control of cell proliferation. However, despite this progress, fundamental questions remain unanswered, such as the problem of how the size of a growing organ could be monitored to determine the appropriate time for terminating growth. While genetic analysis will undoubtedly continue to advance our knowledge about size control in plants, a deeper understanding of this and other basic questions will require including advanced live-imaging and mathematical modeling, as impressively demonstrated by some recent examples. This should ultimately allow the comparison of the mechanisms underlying size control in plants and in animals to extract common principles and lineage-specific solutions.},
  language  = {en}
}
@misc{NowakRussoSchlapbachetal.2015,
  author    = {Nowak, Michael D. and Russo, Giancarlo and Schlapbach, Ralph and Huu, Cuong Nguyen and Lenhard, Michael and Conti, Elena},
  title     = {The draft genome of Primula veris yields insights into the molecular basis of heterostyly},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe},
  number    = {879},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43508},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435088},
  pages     = {19},
  year      = {2015},
  abstract  = {Background The flowering plant Primula veris is a common spring blooming perennial that is widely cultivated throughout Europe. This species is an established model system in the study of the genetics, evolution, and ecology of heterostylous floral polymorphisms. Despite the long history of research focused on this and related species, the continued development of this system has been restricted due the absence of genomic and transcriptomic resources. Results We present here a de novo draft genome assembly of P. veris covering 301.8 Mb, or approximately 63\% of the estimated 479.22 Mb genome, with an N50 contig size of 9.5 Kb, an N50 scaffold size of 164 Kb, and containing an estimated 19,507 genes. The results of a RADseq bulk segregant analysis allow for the confident identification of four genome scaffolds that are linked to the P. veris S-locus. RNAseq data from both P. veris and the closely related species P. vulgaris allow for the characterization of 113 candidate heterostyly genes that show significant floral morph-specific differential expression. One candidate gene of particular interest is a duplicated GLOBOSA homolog that may be unique to Primula (PveGLO2), and is completely silenced in L-morph flowers. Conclusions The P. veris genome represents the first genome assembled from a heterostylous species, and thus provides an immensely important resource for future studies focused on the evolution and genetic dissection of heterostyly. As the first genome assembled from the Primulaceae, the P. veris genome will also facilitate the expanded application of phylogenomic methods in this diverse family and the eudicots as a whole.},
  language  = {en}
}
@misc{JantzenLynchKappeletal.2019,
  author    = {Jantzen, Friederike and Lynch, Joseph H. and Kappel, Christian and H{\"o}fflin, Jona and Skaliter, Oded and Wozniak, Natalia Joanna and Sicard, Adrien and Sas, Claudia and Adebesin, Funmilayo and Ravid, Jasmin and Vainstein, Alexander and Hilker, Monika and Dudareva, Natalia and Lenhard, Michael},
  title     = {Retracing the molecular basis and evolutionary history of the loss of benzaldehyde emission in the genus Capsella},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {775},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43754},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-437542},
  pages     = {1349 -- 1360},
  year      = {2019},
  abstract  = {The transition from pollinator-mediated outbreeding to selfing has occurred many times in angiosperms. This is generally accompanied by a reduction in traits attracting pollinators, including reduced emission of floral scent. In Capsella, emission of benzaldehyde as a main component of floral scent has been lost in selfing C. rubella by mutation of cinnamate-CoA ligase CNL1. However, the biochemical basis and evolutionary history of this loss remain unknown, as does the reason for the absence of benzaldehyde emission in the independently derived selfer Capsella orientalis. We used plant transformation, in vitro enzyme assays, population genetics and quantitative genetics to address these questions. CNL1 has been inactivated twice independently by point mutations in C. rubella, causing a loss of enzymatic activity. Both inactive haplotypes are found within and outside of Greece, the centre of origin of C. rubella, indicating that they arose before its geographical spread. By contrast, the loss of benzaldehyde emission in C. orientalis is not due to an inactivating mutation in CNL1. CNL1 represents a hotspot for mutations that eliminate benzaldehyde emission, potentially reflecting the limited pleiotropy and large effect of its inactivation. Nevertheless, even closely related species have followed different evolutionary routes in reducing floral scent.},
  language  = {en}
}
@misc{JantzenWozniakKappeletal.2019,
  author    = {Jantzen, Friederike and Wozniak, Natalia Joanna and Kappel, Christian and Sicard, Adrien and Lenhard, Michael},
  title     = {A high‑throughput amplicon‑based method for estimating outcrossing rates},
  series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe},
  number    = {745},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43565},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-435657},
  pages     = {14},
  year      = {2019},
  abstract  = {Background: The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCRgenotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming. Results: We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd's Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons. Conclusions: This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.},
  language  = {en}
}
@misc{JohnsonRammKappeletal.2015,
  author    = {Johnson, Kim L. and Ramm, Sascha and Kappel, Christian and Ward, Sally and Leyser, Ottoline and Sakamoto, Tomoaki and Kurata, Tetsuya and Bevan, Michael W. and Lenhard, Michael},
  title     = {The tinkerbell (tink) mutation identifies the dual-specificity MAPK phosphatase INDOLE- 3-BUTYRIC ACID-RESPONSE5 (IBR5) as a novel regulator of organ size in Arabidopsis},
  series = {PLoS ONE},
  journal   = {PLoS ONE},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-410245},
  pages     = {17},
  year      = {2015},
  abstract  = {Mitogen-activated dual-specificity MAPK phosphatases are important negative regulators in the MAPK signalling pathways responsible for many essential processes in plants. In a screen for mutants with reduced organ size we have identified a mutation in the active site of the dual-specificity MAPK phosphatase INDOLE-3-BUTYRIC ACID-RESPONSE5 (IBR5) that we named tinkerbell (tink) due to its small size. Analysis of the tink mutant indicates that IBR5 acts as a novel regulator of organ size that changes the rate of growth in petals and leaves. Organ size and shape regulation by IBR5 acts independently of the KLU growth-regulatory pathway. Microarray analysis of tink/ibr5-6 mutants identified a likely role for this phosphatase in male gametophyte development. We show that IBR5 may influence the size and shape of petals through auxin and TCP growth regulatory pathways.},
  language  = {en}
}
@misc{BreuningerLenhard2017,
  author    = {Breuninger, Holger and Lenhard, Michael},
  title     = {Expression of the central growth regulator BIG BROTHER is regulated by multiple cis-elements},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400971},
  pages     = {10},
  year      = {2017},
  abstract  = {Background Much of the organismal variation we observe in nature is due to differences in organ size. The observation that even closely related species can show large, stably inherited differences in organ size indicates a strong genetic component to the control of organ size. Despite recent progress in identifying factors controlling organ growth in plants, our overall understanding of this process remains limited, partly because the individual factors have not yet been connected into larger regulatory pathways or networks. To begin addressing this aim, we have studied the upstream regulation of expression of BIG BROTHER (BB), a central growth-control gene in Arabidopsis thaliana that prevents overgrowth of organs. Final organ size and BB expression levels are tightly correlated, implying the need for precise control of its expression. BB expression mirrors proliferative activity, yet the gene functions to limit proliferation, suggesting that it acts in an incoherent feedforward loop downstream of growth activators to prevent over-proliferation. Results To investigate the upstream regulation of BB we combined a promoter deletion analysis with a phylogenetic footprinting approach. We were able to narrow down important, highly conserved, cis-regulatory elements within the BB promoter. Promoter sequences of other Brassicaceae species were able to partially complement the A. thaliana bb-1 mutant, suggesting that at least within the Brassicaceae family the regulatory pathways are conserved. Conclusions This work underlines the complexity involved in precise quantitative control of gene expression and lays the foundation for identifying important upstream regulators that determine BB expression levels and thus final organ size.},
  language  = {en}
}